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28 March 2024 |
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Meraculous2: fast accurate short-read assembly of large polymorphic genomes | Jarrod A. Chapman
; Isaac Y. Ho
; Eugene Goltsman
; Daniel S. Rokhsar
; | Date: |
3 Aug 2016 | Abstract: | We present Meraculous2, an update to the Meraculous short-read assembler that
includes (1) handling of allelic variation using "bubble" structures within the
de Bruijn graph, (2) improved gap closing, and (3) an improved scaffolding
algorithm that produces more complete assemblies without compromising
scaffolding accuracy. The speed and bandwidth efficiency of the new parallel
implementation have also been substantially improved, allowing the assembly of
a human genome to be accomplished in 24 hours on the JGI/NERSC Genepool system.
To highlight the features of Meraculous2 we present here the assembly of the
diploid human genome NA12878, and compare it with previously published
assemblies of the same data using other algorithms. The Meraculous2 assemblies
are shown to have better completeness, contiguity, and accuracy than other
published assemblies for these data. Practical considerations including
pre-assembly analyses of polymorphism and repetitiveness are described. | Source: | arXiv, 1608.1031 | Services: | Forum | Review | PDF | Favorites |
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